Facioscapulohumeral muscular dystrophy (FSHD) is a dominantly inherited muscular disorder and the gene for FSHD has been mapped to chromosome 4q35. Recently, the DNA rearrangements associated with the disease were found in the EcoRI fragment detected by the probes p13E-11 and pFR-1, and deletions of the 3.3-kb KpnI repeat units within the EcoRI fragment are thought to cause the disease. In this study, we cloned the FSHD-associated EcoRI fragments (the shortest fragments identified to date: 10 kb) from 2 severely affected patients (unrelated). Restriction enzyme maps of the genomic fragments in the 2 patients revealed that the 10 kb fragments were identical and contained only one 3.3-kb KpnI repeat unit. These results suggest that deletions of the 3.3-kb KpnI repeat units are likely to associate with FSHD, and that the 10 kb fragments may provide a means of understanding the molecular details involved at the site of the chromosomal rearrangements in FSHD.